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In the second episode of The Association for Mass Spectrometry & Advances in the Clinical Lab (MSACL) podcast, namely Getting going with mass spectrometry : Josh learns chromatography (aired 2021-01-07), Dr. Russell Grant mentioned the following tip at 01:03:11 (I apologize in advance for any inaccuracies in the transcript):

The other thing that is often forgotten there is that you can drop the capillary voltage to zero. It's not as good as the diverter valve, but you are not going to be pulling the stuff towards the mass-spectrometer. If you only have a couple of windows and a bunch of junk, you can just keep capillary voltage on during these desired windows and save your diverter valves' maintenance time because they can become maintenance-limiting.

I would think it would lead to a more frequent cleaning of the ionization chamber. Is the gain in postponed maintenance of a diverter valve really worth it?

Are there any other use cases when disabling capillary voltage could be a superior alternative to using a diverter valve?

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I think there is no perfect answer to this situation. In general when the flow is stopped to any detector in an HPLC experiment, there is a change in baseline, and when the flow is re-started, ghost peaks appear in chromatogram. I am talking about optical detectors such as UV, fluorescence, refractive index etc. Same thing happens in MS and perhaps LC ESI-MS is not an exception, in the sense that diverting the flow can lead to the appearance of so-called "ghost" peaks or raised baseline. I have seen that in GC-MS experiments where a change in flow causes weird baseline shifts. This is an interesting phenomenon worth investigating.

So the authors suggest that let us continue the flow, but let us stop the ionization process so that the junk does not go inside the quadrupoles and stay there forever. It is always easy the clean the external ESI system but the internal system needs professional service.

Someone talks about these problems in this forum Diverter valve issues

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    $\begingroup$ Great point about the ghost peaks. I suspected that alternating the flow could have an impact on registration, but I wasn't sure how to clearly articulate this effect. $\endgroup$
    – andselisk
    Feb 12, 2021 at 5:45

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